QC_missing: Missing value for marker or genotype
In vincentgarin/GWASToolBox: GWAS analysis

Description Usage Arguments Value Author(s) Examples

Identify markers or genotypes with a missing rate higher than the specified threshold.

1	QC_missing(mk.mat, threshold = 0.1, MARGIN = 2)

`mk.mat`	`Character` marker score `matrix` with genotype as row and marker as column. Rows and columns names must be the genotype and marker identifiers respectively. Missing values must be coded `NA`.
`threshold`	`Numeric` value representing the missing values rate above which a marker or a genotype is considered as problematic. Default = 0.1.
`MARGIN`	`Numeric` value giving the subscript which the function will be applied over. If MARGIN = 1, the function looks at the genotypes (rows). If MARGIN = 2, the function looks at the markers (columns). Default = 2.

Return:

mis.ind

Three columns data.frame with: 1) marker or genotype names; 2) column or row positions in the matrix; and 3) The percentages of missing values.

Vincent Garin

data('USNAM_geno')

# missingness of markers
QC_missing(mk.mat = USNAM_geno)

# missingness of genotypes
QC_missing(mk.mat = USNAM_geno, threshold = 0.2, MARGIN = 1)